Methods

Data was processed using CAPHEINE v1.1 , which was written using the nf-core pipeline framework (Ewels et al., 2020). CAPHEINE utilises reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v25.04.6 (Di Tommaso et al., 2017) with the following command:

nextflow run CAPHEINE -c CAPHEINE/conf/silverback_arm.config --reference_genes /home/hverdonk/GCF_000864105.1_noTerminalStopCodon.fasta --unaligned_seqs /home/hverdonk/h5n1_outbreakSeqs.fasta --foreground_regexp cattle --outdir CAPHEINE-H5N1

Tools used in the workflow included: BioPython (Cock et al., 2009) BUSTED (Murrell et al., 2015) Cawlign Contrast-FEL (Kosakovsky Pond et al., 2020) DRHIP FEL (Kosakovsky Pond et al., 2005) HyPhy (Kosakovsky Pond et al., 2019) IQ-TREE (Minh et al., 2020) MEME (Murrell et al., 2012) MultiQC (Ewels et al., 2016) PRIME RELAX (Wertheim et al., 2014) SeqKit (Shen et al., 2024) .

References

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